[gmx-users] Problem in energy minimization for a empty membrane system
Bing Bing
jarbing09 at gmail.com
Tue Jun 23 16:46:27 CEST 2009
Thanks for reply.
I've used editconf to define the box by issuing :-
editconf -f popc.pdb -o popc_box.gro -c -d 1.0 -bt cubic
Is this the correct way of using editconf?
And with this i proceed with grompp with the mdp file from previous email
followed by mdrun....
Actually the restraint is require in another system (membrane+protein), i
wanted to test it out in the this smaller systme before using it in the
complete systme.However, it failed.
Thanks in advance
regards,
bing
On Tue, Jun 23, 2009 at 10:21 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> Bing Bing wrote:
>
>> Hi Justin,
>> I've tried with no restraint and the minimization stopped at the same
>> time. I actually suspect that the restraint is not working at all. My top
>> file is as below:-
>> #include "ffG53a6_lipid.itp"
>> #include "popc.itp"
>> #ifdef POSRES
>> #include "posres_popc.itp"
>> #endif
>> #ifdef FLEX_SPC
>> #include "flexspc.itp"
>> #else
>> #include "spc.itp"
>> #endif
>>
>> [ system ]
>> ; name
>> Pure POPC bilayer with 128 lipids 2460 water
>>
>> [ molecules ]
>> ; name number
>> POPC 128
>> SOL 2460
>>
>> my posres_popc.itp is as below:-
>> [ position_restraints ]
>> ; atom type fx fy fz
>> 1 1 1000 1000 1000
>> .....
>> 51 1 1000 1000 1000
>> 52 1 1000 1000 1000
>>
>> my mdp file as below :-
>> define = -DPOSRES
>> integrator = steep
>> emtol = 1000
>> emstep = 0.01
>> nsteps = 100
>> rlist = 1.2
>> coulombtype = PME
>> rcoulomb = 1.2
>> rvdw = 1.2
>> constraints = none
>>
>> May i know that is the top, posres and also the mdp file correctly done?
>>
>
> Well, they are syntactically correct, it seems. I see no purpose in
> restraining lipids during a minimization, however.
>
> And by looking at the log file in the previous mail, is it confirm that it
>> manage to read the restraint file?
>>
>
> Can't tell. Your system is crashing instantly for some reason.
>
> The starting structure is taken from Peter Tielemen website and what i did
>> is editconf to make box and i didn't solvate because the starting structure
>> come together with water. I'm not sure this is the correct way of doing it.
>> Please advice.
>>
>
> Please define "editconf to make box" - have you somehow manipulated the
> structure? That could be a source of error. The structure that Tieleman
> provides minimized for me with no problem when I used it recently.
>
> -Justin
>
>
>>
>> Thanks in advance.
>> Bing
>>
>>
>>
>> On Tue, Jun 23, 2009 at 7:16 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> jalemkul at vt.edu>> wrote:
>>
>>
>>
>> Bing Bing wrote:
>>
>> Hi! I'm a postgraduate student from Malaysia and currently
>> facing energy minimization problem for my membrane system.
>> I'm trying to perform energy minimization for an empty POPC
>> membrane with position restraint on the lipid. Minimization stop
>> due to inf Fmax. And I noticed that in the log file as below:-
>> Initiating Steepest Descents
>> Max number of connections per atom is 25
>> Total number of connections is 84976
>> Max number of graph edges per atom is 4
>> Total number of graph edges is 22896
>> Going to use C-settle (2460 waters)
>> wo = 0.333333, wh =0.333333, wohh = 3, rc = 0.08165, ra = 0.0384897
>> rb = 0.0192448, rc2 = 0.1633, rone = 1, dHH = 0.1633, dOH = 0.1
>> Started Steepest Descents on node 0 Tue Jun 23 17:03:43 2009
>> Steepest Descents:
>> Tolerance (Fmax) = 1.00000e+03
>> Number of steps = 100
>> Grid: 11 x 11 x 11 cells
>> Step Time Lambda
>> 0 0.00000 0.00000
>> Energies (kJ/mol)
>> Bond Angle Proper Dih. Ryckaert-Bell.
>> Improper Dih.
>> 1.64082e+05 1.71875e+04 4.06560e+03 6.45104e+03
>> 8.36392e+03
>> LJ-14 Coulomb-14 LJ (SR) Coulomb (SR)
>> Coul. recip.
>> 2.12067e-314 2.12067e-314 -1.58963e+04 -1.05392e+05
>> -1.15292e+05
>> Position Rest. Potential Pressure (bar)
>> 0.00000e+00 -3.64297e+04 nan
>>
>>
>> >From the looks of some of these energies (i.e., LJ-14,
>> Coulomb-14), it looks like something is severely wrong with your
>> starting structure, and applying position restraints probably isn't
>> helping.
>>
>> Try the minimization without restraints and see if it works.
>>
>> Also, have you set the appropriate "define" line in the .mdp file,
>> corresponding to what is prescribed in the .top?
>>
>> -Justin
>>
>> -------------------------------------------------------
>> Program mdrun_d, VERSION 4.0.5
>> Source code file: nsgrid.c, line: 357
>> Range checking error:
>> Explanation: During neighborsearching, we assign each particle
>> to a grid
>> based on its coordinates. If your system contains collisions or
>> parameter
>> errors that give particles very high velocities you might end up
>> with some
>> coordinates being +-Infinity or NaN (not-a-number). Obviously,
>> we cannot
>> put these on a grid, so this is usually where we detect those
>> errors.
>> Make sure your system is properly energy-minimized and that the
>> potential
>> energy seems reasonable before trying again.
>> Variable ci has value -2147483648. It should have been within [
>> 0 .. 1331 ]
>> the position restraint energy is 0 as highlighted. Here's the
>> position restraint file :-
>> [ position_restraints ]
>> ; atom type fx fy fz
>> 1 1 1000 1000 5000
>> 5 1 1000 1000 1000
>> 6 1 1000 1000 1000
>> 7 1 1000 1000 1000
>> 8 1 1000 1000 1000
>> 9 1 1000 1000 1000
>> 10 1 1000 1000 1000
>> ......
>>
>> whereby the restraint energy is 1000kcal/mol in x, y and z
>> plane. In the log file the position restraint energy is stated
>> as 0.0000e+00 (as highlighted above).
>> I think that the position restraint is not working fine here. Is
>> there anyways to solve this? did I miss out something here?
>> I would be grateful if anyone can advice me on this.
>>
>>
>> ------------------------------------------------------------------------
>>
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>>
>> -- ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
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>>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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